Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

70 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of Arabidopsis thaliana columbia and DEWAX2 overexpression plants line stems

ABSTRACT: The experiment was designed to enable comparison between Arabidopsis thaliana columbia and DEWAX2 OX plants line.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hyojin Kim

PROVIDER: E-MTAB-5980 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Transcription profiling by array of A. thaliana columbia stems after treatment of hypoxia to investigate genome-wide gene expression analysis

Project description:The experiment was designed to enable comparison between Arabidopsis stems treated hypoxia and Arabidopsis stems treated normoxia.

2015-12-31 | E-MTAB-3510 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis thaliana Columbia and MYB94 over expressing plant line leaves to investigate genome wide gene expression analysis

Project description:The experiment was designed to enable comparison between columbia and MYB94 OX plants line Arabidopsis leaves

2015-04-14 | E-MTAB-2870 | biostudies-arrayexpress

Genome-wide gene expression analysis of DEWAX OX plant lines compared to wild type

Project description:The experiment was designed to enable comparison between columbia and DEWAX OX plants line Arabidopsis stems

2013-12-01 | E-MEXP-3781 | biostudies-arrayexpress

Gene expression profiling of Arabidopsis Atwrky12 mutants stems

Project description:Gene expression profile in Arabidopsis stems of T-DNA insertion lines Atwrky12-1 and Atwrky12-2 were compared with Columbia wild-type plants at 45 days after germination.

2011-06-01 | E-MEXP-2792 | biostudies-arrayexpress

Next-generation sequencing analyses of the differently expressed genes of wild type and atcep1 mutant Arabidopsis thaliana

Project description:Purpose: The goal of this study is to compare the differently expressed genes in the wild type and the KDEL-tailed cysteine protease AtCEP1 knockout (atcep1) Arabidopsis using RNA-sequencing (RNA-seq). Methods: Arabidopsis buds mRNA profiles of anther development stages 5-6, 7-9, and 10-11 of the wild type (WT) and atcep1 mutant were generated by deep sequencing via Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with the following steps: Remove reads with adaptor sequences; Remove reads in which the percentage of unknown bases (N) is greater than 10%; Remove low quality reads, in which the percentage of the low quality base (base with quality value â¤ 5) is greater than 50%. The clean reads were mapped to the Arabidopsis reference genome and reference genes using SOAP aligner/SOAP2. No more than 2 mismatches were allowed in the alignment. The gene expression level was calculated using RPKM (Reads Per Kb per Million reads). Differential expression analysis between the wild type and the atcep1 mutant was performed using the DEGseq R package (1.12.0) based on normalized read counts. A corrected P value of < 0.005 and |log2Ratio| > 1 were set as the threshold for significantly differential expression. Results: We identified 872 genes showing significant differential expression, and in the atcep1 mutant, the upregulated genes significantly outnumbered the downregulated genes at the three time points. The GO analysis of the differently expressed genes showed that the expression of genes participating in anther tapetal secretory structure formation, pollen wall development, and tapetal cell wall generation, clearly changed. Arabidopsis buds mRNA profiles of development stages 5-6, 7-9, and 10-11 of the wild type (WT) and atcep1 muant were generated by deep sequencing via Illumina HiSeqTM 2000.

2016-03-25 | E-GEOD-50956 | biostudies-arrayexpress

RNA-seq of Arabidopsis thaliana spms and wild-type plants inoculated with Pst DC3000 or mock

Project description:RNA-seq of Arabidopsis thaliana spermine synthase (spms) mutant and wild-type (Col-0) inoculated with Pseudomonas syringae pv. tomato DC3000 or mock (MgCl2)

2023-08-31 | E-MTAB-13086 | biostudies-arrayexpress

Molecular characterization of the submergence response of Arabidopsis thaliana ecotype Columbia

Project description:This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level. 20 samples, 5 conditions (7 h submergence in darkness, 7 h darkness, 24 h submergence in darkness, 24 h darkness, 0 h light control), 2 RNA pools (rosette leaf and root tissues), 2 independent biological replicate experiments

2010-11-12 | E-GEOD-24077 | biostudies-arrayexpress

RNA-seq of Arabidopsis thaliana plants treated with putrescine, spermine, flg22 and combinations

Project description:RNA-seq of Arabidopsis thaliana plants (Col-0) treated with putrescine (100 µM), spermine (100 µM), flg22 (1 µM) and combinations (putrescine + flg22; spermine + flg22)

2022-10-20 | E-MTAB-11820 | biostudies-arrayexpress

Expression data from Wild type (WT) and AtCBF1 OX potato plants exposed to different abiotic stresses

Project description:Potato plants are sensitive to multiple abiotic stresses such as drought, low temperature and high light. We analyzed the transcriptome of WT potato plants as well as that of transgenic potato plants expressing the Arabidopsis stress related transcription factor CBF1 that confers tolerance to multiple stresses. Wild type and AtCBF1OX transgenic potato plants were exposed to low temperature, high light, drought or kept under control conditions as described below in detail, and transcriptional changes induced by the different stresses were analyzed.

2015-03-01 | E-GEOD-61004 | biostudies-arrayexpress

Transcriptome profiling from roots of jatropha in response to waterlogging

Project description:Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging. 4 samples, 2 conditions (24 h nonstress and 24 h waterlogging stress) and 2 independent biological replicates of 2 mRNA pools

2014-11-05 | E-GEOD-57428 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data